Protocol
by Del Rion
Summary: Considering his past with S.H.I.E.L.D., Tony has difficulties following certain rules. Fury does not appreciate this and attempts to use Pepper to convey his feelings to Mr. Stark – only to be informed that he should look in the mirror before making such requests. It would also seem J.A.R.V.I.S. has the strongest moral compass of them all – at least in theory. (Genius, AI & Bots)


**Story Info**

 **Title:** Protocol

 **Author:** Del Rion

 **Fandom:** Iron Man (MCU)

 **Timeline:** after 'The Avengers' and 'Iron Man 3'

 **Genre:** Drama

 **Rating:** T / FRT

 **Characters:** Nick Fury, J.A.R.V.I.S., Pepper Potts, Tony Stark (Iron Man)

 **Summary:** Considering his past with S.H.I.E.L.D., Tony has difficulties following certain rules. Fury does not appreciate this and attempts to use Pepper to convey his feelings to Mr. Stark – only to be informed that he should look in the mirror before making such requests. It would also seem J.A.R.V.I.S. has the strongest moral compass of them all – at least in theory.  
Complete. Part of "Genius, AI & Bots" series.

 **Written for:** a prompt on **avengerkink** (avengerkink . livejournal dot c0m/ 16019 . html ?thread=34768275).

 **Warnings:** Language.

 **Disclaimer:** Iron Man, Avengers and Marvel Cinematic Universe, including characters and everything else, belong to Marvel, Marvel Studios, Jon Favreau, Joss Whedon, Shane Black, Paramount Pictures and Walt Disney Studios Motion Pictures. In short: I own nothing; this is pure fiction created to entertain likeminded fans for no profit whatsoever.

 **Beta:** Mythra (mythras-fire)

* * *

 **About** ** _Protocol_** **:** Based on the following prompt on **avengerkink** :

 **Tony & S.H.I.E.L.D., Do as I Say Not as I Do doesn't work on Tony Stark** (by anonymous)

 _Tony's introduction to S.H.I.E.L.D. was peppered with people breaking into his home right after he was almost killed in a home invasion (by someone in his closest circle), an agent infiltrating his company and maneuvering to gain his trust only to stab him in the neck with a syringe full of unknown chemicals. And if Coulson's entrance in the Avengers is any judge they feel free to override his security protocols whenever they want access to him and he doesn't want to see them._

 _This would not leave most people in a good disposition toward the spy organization in general and the agents involved in particular. But Tony is mostly a good sport. He'll bitch and moan and he's slightly weary and unwilling to take most of what they say at face value but he'll work with them and be genuinely friendly and trust them at his back._

 _The problem? They will *never* get him to take them seriously when they talk about need to know, security clearance (his) and how illegal it is to hack into S.H.I.E.L.D.'s server._

* * *

 **Story and status:** Below you see the writing process of the story. If there is no text after the title, then it is finished and checked. Possible updates shall be marked after the title.

 **Protocol**

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. . .

* * *

 **Protocol**

* * *

Tony's half expecting it when the notification window appears on the screen.

 _"Sir, S.H.I.E.L.D. appears to be blocking our efforts to access the file,"_ J.A.R.V.I.S. informs him.

"Bypass them," Tony orders. He could do it himself, but he has an AI who can do it for him, and it's good practice for J.A.R.V.I.S. to flex his artificial muscles occasionally.

The AI proceeds to find another way in – a way that is too fast for S.H.I.E.L.D.'s security programs and their human users. It's times like these when Tony allows himself to feel smug about his accomplishments, seeing as he created J.A.R.V.I.S. from scratch.

"Is the back door secured?" he asks, though, because he feels he has an obligation to make sure his AI doesn't leave a huge mess, however unlikely that is.

 _"The back door is secure and invisible to any user other than you and myself, sir – which is why S.H.I.E.L.D. has not detected it even though they are aware you hacked into their files during your stay on the Helicarrier. They have performed numerous security sweeps afterwards, but our entry point remains open."_

J.A.R.V.I.S. falls silent and Tony assumes he's busy hunting down the files Tony wants to access – something S.H.I.E.L.D. claims he has no clearance for. After everything that has transpired, Tony won't let those bureaucratic statements fool him: he helped save the world, almost sacrificing his life in the process, and he deserves some goddamn credit for that.

Plus, as far as he's concerned, it's all give and take, and S.H.I.E.L.D. established their methods long before Tony even wanted to work in tandem with them.

"Give as good as you get," he mutters.

 _"I have accessed the files, sir,"_ J.A.R.V.I.S. notifies him.

"Download to my private server," Tony orders needlessly.

 _"At once, sir,"_ the AI acknowledges, then questions: _"Sir?"_

"Yeah?"

 _"I feel obligated to ask whether it is morally sound to access S.H.I.E.L.D. files in this fashion when we are supposed to be working in cooperation with them?"_

"You didn't miss their last big speech about how I didn't have a high enough clearance, did you?"

 _"You know I did not, sir."_

"Then you have your answer."

J.A.R.V.I.S. considers that for a moment. _"If I understand S.H.I.E.L.D.'s stand on the matter, they do not want you poking around files not pertaining to your contract with them."_

"It's not a contract," Tony corrects. "It's… a mutual agreement, at best. They need things from me, and I'm deigning to give those things to them."

 _"Be that as it may, you are breaching protocol by breaking into classified S.H.I.E.L.D. files – which they have repeatedly attempted to stop you from doing, as you well know."_

"What's your point, J? That we're playing nice with the Super Spies while breaking the rules behind their backs?"

 _"Something along those lines, sir."_

"Well, they started it, and I need those files," Tony shrugs.

J.A.R.V.I.S. restrains himself from saying the word 'childish' out loud, even though Tony is certain it is at the very front of his artificial mind. The AI knows what Tony means, and it is not that he is shocked by S.H.I.E.L.D.'s various breaches of his privacy. He has learned by now how they operate, and why they think it is the best – and sometimes only – way to execute their directive to secure the world. Yet by forcing those methods on Tony, they have crossed a line and lost the right to dictate how Tony is supposed to react.

Tony will not stick to the rulebook if no one else does.

* * *

"Miss Potts," a man with an eye patch greets Pepper as she meets him in the lobby. "I am glad you could find a moment to meet me in person."

"Of course, Director," Pepper nods her head and shakes his hand. Her grip is firmer than his. "Shall we go to my office?"

"Please," Nick Fury inclines his head and allows her to lead the way.

After they have sat down and Pepper's secretary has brought them a tray with cups of coffee, milk and sugar, a certain tensions descends upon the room. Fury is attempting to play nice while Pepper can tell he's not happy to be here.

"How can I help you, Director?" Pepper asks to move things along. "Is there anything S.H.I.E.L.D. needs that we have not already discussed?"

"My visit pertains to a more… personal matter," Fury confesses. "You may be aware that Tony Stark has been working in conjunction with S.H.I.E.L.D. since the Battle of New York."

"I am aware," Pepper nods.

"We have allowed him certain freedoms within S.H.I.E.L.D., for him to be able to work on the projects we have agreed upon, but in the last week alone there have been five breaches of our security by Mr. Stark."

"I hope you have proof, whether you are accusing him or Stark Industries," Pepper states coolly.

"Oh, I know it's Stark," Fury replies, leaning back in his chair, hands folded over his stomach. He's trying to appear nonthreatening, but it works only so well, given the topic of their conversation. "He has a certain… way of doing things. We can already recognize the pattern he uses."

"Yet you have not been able to stop him," Pepper guesses.

"If it were anyone else, we would have already put a stop to it," Fury notes. If it is meant to be a threat or a display of mercy, she is not certain. "As it is, Stark is an ally we want to keep on our side, but it seems he does not grasp the concept of security clearances and why those measures are in place."

"I am certain you are not going to enlighten me on the matter."

"I'm afraid not, but you are a sensible, smart person, controlling one of the largest, most secure companies in the world – and I know you appreciate things being done in a certain way. Even when it comes to Tony Stark."

"If you want me to go and tell him to stop poking holes in your firewall, you are wasting your breath: if Tony's bothering to break into your files, he is looking for something. Until he's found it, no one can deter him." Before, a firm command may have worked, but after becoming Iron Man, Tony's priorities and methods had shifted and Pepper knows where her influence ends.

"S.H.I.E.L.D. handles sensitive information – has done so since it was founded. We cannot have one of our civilian consultants constantly breaking the rules and going through data not meant for him," Fury states.

Pepper raises her eyebrow at the word 'civilian', even though Tony is, for all intents and purposes, an untrained, unqualified man flying in a highly advanced, weaponized suit of armor. That is a moot point, however, and Fury has to know that.

"What is it that you want from me, Director?" Pepper asks bluntly.

"The means to make Stark stop before he unearths something he should not. To explain to him that there are protocols he needs to follow if he wants access to information beyond his security clearance."

"You want him to play by your rules," Pepper translates and has to give the man a wry smile. "The way you have always respected Tony's privacy and followed good conscience when it comes to dealing with him?"

Fury's mouth tightens. "You know Stark cannot be dealt with like most people."

"That does not warrant breaking into his home, or sending undercover agents to worm their way into his life – and into his company," Pepper snaps. "I know how Tony works. I have worked with him for a long time, and I have been there from day one when he first built the suit in his workshop and started trying to do the right thing. I may have not always agreed, but compared to his shortcomings when it comes to following the rules… I think S.H.I.E.L.D. and its director could take a moment and reflect upon their own actions and ponder whether one thing may have influenced the other."

There is not much to be said after that.

Fury leaves before he has even touched his coffee, and Pepper decides to stop by a Starbucks on her way to Malibu; she's in need of a sugary-sweet Frappuccino before taking this any further.

* * *

Tony is in his workshop when Pepper arrives, sipping the last of her salted caramel mocha.

"Hey, Pep," Tony greets, attention focused on the holographic screens before him. One of them may be the new repulsor system he is designing for the S.H.I.E.L.D. Helicarriers.

"Guess who paid me a visit today?" Pepper starts, walking towards him.

"If that is an accusation that I may have – occasionally – taken a look at your private schedule, in my defense –"

"No," Pepper chuckles, then sighs. "Director Fury wanted to have a word with me, although I got the impression he may have wanted to talk to you even more."

"He has my number," Tony replies then turns his chair around to face Pepper, back straight, legs spread along the seat of the saddle chair. "What did he want?"

"For you to stop breaking into their system," Pepper says.

Tony scoffs. "Like that's going to happen before he gives me the clearance I deserve, and he knows it."

Pepper doesn't want to imagine what Fury thinks Tony might find that would be so dangerous – or whether it is just something that would make S.H.I.E.L.D. look bad. "In the interest of staying on their good side, perhaps you should at least try and hide your activities better," she suggests.

Tony's expressions shifts. "And here I was thinking you would tell me to stop."

"Would you?"

"No."

"Then just hide your trail. I know you can do that," Pepper presses.

Tony shrugs. "They have heightened their security, which is good for them. Not good enough to keep the world's most advanced AI out, though."

Pepper isn't certain why she feels the need to disapprove. "You are using J.A.R.V.I.S. to break into S.H.I.E.L.D.'s files?"

Again, Tony shrugs. "Why not? He gets the job done, and besides, I can't be expected to do everything myself. I do have an R&D department to run, after all…"

Pepper does not take the bait. "Why do I get the feeling that you are purposefully using J.A.R.V.I.S. because S.H.I.E.L.D. has hacked him so many times in the past?"

"Twice," Tony corrects her, as if the actual number makes it better. "Twice is too much," he adds, confirming her suspicion even before he states a second later: "That's not why I'm making J do it. It's simply more efficient."

J.A.R.V.I.S. remains silent, as if the AI knows better than to offer his own opinion. Pepper believes he does have an opinion, after all, but J.A.R.V.I.S. will follow Tony to his grave if need be, his loyalty running deeper than gigabytes of programming, and no matter his formal protests – if there have been any – J.A.R.V.I.S. will always do what Tony tells him to.

Whether that is terrifying or awe-inspiring, she is not certain.

She does know, however, that Tony's methods of breaking into S.H.I.E.L.D. are better kept between them, seeing as S.H.I.E.L.D. would never pass up on the opportunity to exploit J.A.R.V.I.S.'s capacity for destruction – or his usefulness in their hands – if they knew just how capable the AI was.

After all, Hell hath no fury like Tony Stark when someone is trying to take away something that is his – something that he views as _family_.

 **The End**


End file.
